#HappyMicroscopyMonday #microscopycommunity- Wayne S. Rasband Open Source Imaging Award recognizes individuals advancing open source imaging software or hardware by making tools freely accessible, modifiable, and impactful.
Nominate or apply by May 1, 2026!
buff.ly/5DYr7UO
Happening now! We are kicking off the Image Data Community Days - a full week of online workshops & events. Hope you can join us to talk about image data topics! #ImagingCommunity
Register & more info⤵️
www.eurobioimaging.eu/events/image...
We tracked a zebrafish tail tip for 30h of light-sheet imaging.
It didn’t exist at t=0.
LiLiTTool: CoTracker3 + object detection → real-time microscope steering.
3D, multi-ROI, open source.
www.biorxiv.org/content/10.6...
#bioimaging #lightsheet
thanks @jytinevez.bsky.social
#microscopycommunity- looking for help on your image analysis? GloBIAS offers free help sessions!
Dates: 20-24 April 2026
Registration deadline: 15 April 2026
Registration may close earlier if all available slots are filled.
Register here buff.ly/KzgIYOd
More information: buff.ly/vaCW4sF
👀 Check out the amazing plenary sessions & workshops during our 5-day long Image Data Community Days event! There's something for everyone - don't miss out.
Registration is FREE & open to all⤵️
www.eurobioimaging.eu/events/image...
We will be there with @gaellel.bsky.social, Thierry Pécot and myself to present F-BIAS, and the novel tool created by Gaëlle: EpiCure github.com/Image-Analys...
I think this is probably the future of 3D microscopy data exploration.
Just browse the data tight away.
I was recently looking into WebGPU, but seems like this project already can work with Zarr
Incroyable!!
Volume Rendering - Chameleon
Volume Rendering - Chameleon
Volume Rendering - Chameleon
Volume Rendering - Chameleon
Meet Kilian.
A 2 GB CT scan of a chameleon — rendering in the browser in a few hundred milliseconds.
Built with Kiln: a WebGPU-native out-of-core volume renderer.
Bricked volume storage, GPU memory virtualization, LRU streaming, compute shader ray marching.
Open source:
github.com/MPanknin/kil...
I'm happy to present our new tool, EpiCure, a napari plugin to ease correction of segmentation and tracking of epithelia movies, developed in @devstempasteur.bsky.social
Choanoflagellates — our closest animal relatives — form multicellular colonies in two ways: cell division AND aggregation.
This previously unknown "mixed multicellularity" suggests our animal origins are more complex than thought.
📄 @thibautbrunet.bsky.social ↘️
Take advantage of this amazing offer to get FREE image analysis support from the experts at @globias.bsky.social🔬 !
Image analysis. (A) Pie chart shows the % of facilities with dedicated image analysis support. Yes (blue), no (orange). (B) Violin plot shows the distribution of # FTE providing that support. Mean and standard deviation are included. (C) Pie chart shows the % of facilities providing bespoke image analysis. Yes (blue), no (orange). (D) Pie chart shows the sources of cost recovery of bespoke image analysis support. Uncharged (blue), charged by the hour (orange), project fee (green), staff salary contribution (sky blue). (E) Pie chart shows the % of facilities that support commercial image analysis software. Yes (blue), no (orange). (F) Pie chart shows the sources of funding to maintain commercial analysis software. Mix of all sources (blue), on an annual basis from user charges (orange), institutional support (green), grant funding (sky blue), on an ad hoc basis from user charges (magenta). https://onlinelibrary.wiley.com/doi/10.1111/jmi.70079
Little bit surprised to see most microscopy facilities now have dedicated image analysis support, but 1.0 FTE on average is nowhere near enough.
And more than half don't charge for analysis services?!?
🤨
onlinelibrary.wiley.com/doi/10.1111/...
Hello from sunny @institutpasteur.bsky.social
Thanks to #Appose hackaton with @jytinevez.bsky.social, @ctrue.bsky.social, @nkiaru.bsky.social, @msphan.bsky.social, @strigaud.bsky.social, Carlos, Thomas and Julie, DeXtrusion can be **INSTALLED** and run to detect cell extrusions directly from Fiji 🤩! Appose is amazing
Yes! We have international students every year. Keep in mind that you need to be able to travel to Paris
(All these courses are built by dedicated people, and are by the way happening in Paris in June, just saying:
Organized by the great Mohamad Harastani and Eduard Baquero from the IAH and the nano imaging core!
This course is designed for PhD students, postdocs, engineers, and researchers in structural biology or cell biology with basic knowledge In SPA or cryo-ET data processing.
The deadline to apply is May 1st 2026
For more information please visit our website: www.pasteur.fr/fr/enseignem...
Participants will learn the core concepts and software tools required to analyze complex 3D data to reveal macromolecular structures directly within their native cellular environments at molecular resolution
3/ Sub-tomogram averaging in cyo-EM
6 - 10th of July 2026
This hands-on course provides in-depth training in processing large-scale cryo-electron tomography (cryo-ET) datasets using subtomogram averaging (STA) — a cutting-edge technique at the interface of structural and cell biology.
The course aims to provide all the theoretical background needed and useful tools to render the trainees autonomous in Electron Tomography.
Registration deadline: April 6, 2026.
www.pasteur.fr/en/education...
Organized by the great Anna Sartori and Anastasia Gazi, from the EM cores of Pasteur!
The course is meant for PhD students, post-doctoral fellows, engineers, and researchers who have some (Cryo-)EM experience and would like to use (Cryo-)ET in the near future. Applicants who already have tilt-series for processing will be prioritized.
Introduction to tomography, frame alignment, tomogram reconstruction, denoising, volume annotation, and particle picking for subtomogram analysis will be covered
This one-week course aims to introduce basic concepts in image analysis and practical experience in tomographic reconstructions for different needs: processing of low-dose tilt series with and without fiducials for 3D volume annotation or subtomogram averaging.
In situ studies can reveal additional important information for macromolecules and their complex environments, their adopted conformations, recruitment on specific sites and interactions with other key molecules or ultrastructure.
Electron tomography, combined with image processing is one of the most powerful methods for studying cellular details in 3D. I
2/ The IPEM-TOMO course:
Cryo-ET : Image Processing for Electron Microscopy/Tomography,
June 8 to 12.
Some impressions from last time
(We had a good time, and aim for it again.)
Organized with the great @biaunit.bsky.social , @gaellel.bsky.social and the IAH team.
